The Greenhouse Effect
by ephemereal
Summary: Post-Revolutions. "You should be dead. But apparently you weren't ready for that, either." Updated: 5-28-05
1. Prologue: A City Made of Light

THE GREENHOUSE EFFECT

Author's Note: So here you have it. My first attempt at a Matrix fic. I've barely read anything, so if my concept is similar to yours, it's not that way on purpose. Let me know and I'll do what I can to make it different. Constructive criticism is welcomed, but please be kind.

Disclaimer: I don't own The Matrix or any of its characters. If you recognize pieces of dialogue, chances are those aren't mine either.

* * *

PROLOGUE

_-We made it._

_-You said we would._

_-It's unbelievable, Trin. Lights everywhere. Like the whole thing was built with light. I wish you could see what I see._

_-You've already shown me so much._

_-What is it, Trinity? What's wrong?_

_-I can't come with you, Neo. I've gone as far as I can._

_-Why? Oh, no. Oh no, no, no._

_-It's all right. It's time. I've done all that I could do. Now you have to do the rest. You have to finish it. You have to save __Zion_

_-I can't. Not without you._

_-Yes, you can. You will. I believe it, I always have._

_-Trinity... Trinity. You can't die. You can't. You can't._

_-Yes, I can. You brought me back once, but not this time._

_The fight, seen through eyes blinded by grief. Pain. Blinding pain. Then darkness._ _Images swam, thoughts, sensations…pieces of life. Pieces of consciousness. It was almost all dark at first, then as time went by—he had no idea how much, for time had no meaning in this place—there began to be flashes of light now and again.__The glittering gold of the machine city, the city of light. The lightning that had lit up the sky that night when it seemed the worlds had converged. __A scruffy looking black cat sat in a patch of early morning sunlight, washing itself. Its eyes shown green, bright green, too bright to be real, but then of course this wasn't real. It couldn't be real. The sun did not shine in the real world. The cat yawned, and its throat seemed to expand somehow, swallowing the world._

_There were bluish sparks in the darkness, the sparks of something dying. A dying machine, a damaged ship. The Logos, he realized, consciousness suddenly filling with the heaviness of dread. He was back here again, this awful place, except now he could see. And though he knew this wasn't real, couldn't be real, it was that much more terrible. _

_The control panels were shattered, coolant leaks spattering glowing liquid into the corridors. It was a broken vessel, gone before its time. Like so much in this useless, meaningless war. He tried desperately to escape the dream, if that was, in fact, what this was, could not bear to see the lifeless form on the floor among the wreckage. But there was nothing he could do. He was utterly helpless against the assault. He wondered for a moment if this was hell, but then he saw, and there was nothing else but pain._

_He could not believe that she was truly gone. She had been there always, from the very beginning, never letting go. She was the voice of reason, the inspiration, the very cause itself. She was never afraid, even at the very end. If it had not been for her, he would not be here now, crouched amidst the wreckage. And if he had never come along—well, he simply could not afford to think of that at the moment._

_A few more seconds passed, then he pushed himself up to his feet, holding onto the wall unsteadily. The smoke was still rising, even half an hour after it had happened. It seeped out of and into everything, engulfing the entire room, and for a moment he thought he could feel it saturating his pores like poison. The filth and pollution that had become the common byproduct of years of war. He ran a hand across his eyes, over his forehead, brushing back strands of sweaty hair, and wiping the hand off on his pants at last, violently, as if trying subconsciously to wipe away the shell of grief that was rapidly hardening around him. He closed his eyes hard, wincing at the sting of dust and chemical residue, wishing that when his vision cleared again, it would tell him that he had been wrong, that this was not real. _

_When he looked down again, he saw the same thing as before—his greatest fear—her body lying there among the wreckage. It seemed to him suddenly that in death she was more beautiful than ever. She had been freed at last from the monumental exhaustion and anxiety of the war. For a moment he felt something almost akin to jealousy; he had wished for such release for such a long time he could hardly remember a time when the longing hadn't been there. He thought for the briefest second of giving in, of lying down beside her and never getting up again, but then he remembered his promise. _

_There were people waiting, thousands of them, for him to bring this war to an end. To free them, like he longed to be freed. He could not break that promise. Even in his grief-shattered state, he was a soldier first. _

_The image blurred, as if with tears, though he could still feel nothing. It dissolved into the familiar green code before his eyes, streaming down like rain, engulfing everything._

_And then suddenly—_

Light. White light. Blindingly, painfully bright light.

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	2. The Call

Author's Note: Thanks to everyone who reviewed the first chapter. I'm spoiled rotten by my other fics, and I'm a total review whore, so it's much appreciated.

As far as this chapter…well, you're not going to understand everything straight from the start, you're going to have to work it out for yourself. But then Matrix fans should be more than capable of that. Just take this as fair warning—I never spoon feed my readers. Because, after all, there is no spoon, right?

Hope you enjoy.

Daydreamer731

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CHAPTER 1

The sentinel's titanium plating gleamed blindingly in a ray of rare sunlight that had managed to make its way through a small hole in the clouds of ash that still blackened the sky despite everyone's best efforts. Every attempt had been made to fix the damage, but the cold hard fact remained—it just wasn't that easy to undo centuries of destruction. They were not ready to give up, though. Far from it.

The sentinel paused at the gathering point, hovered closer to the ground for a moment to seize a young sapling gently in its metal tentacles, then propelled itself back toward the nursery. It maneuvered gracefully past the glass doors and through the pressure zone, then past row upon row of young plants, stopping at last in front of one of the overseers. She was dressed like all the other former resistance soldiers who had been assigned to do surface work, in black pants and a gray wool sweater, but she had removed the sweater in the artificial heat of the greenhouse, revealing a deep blue undershirt. A lock of dark hair fell across her face every few moments, too long to be worn loose, but not yet long enough to be captured in the tie at the nape of her neck. She brushed it back every time it fell, her fingers leaving traces of soil on the pale skin of her face.

The sentinel grasped the tree in two of its tentacles, using a third to gesture at a spot exactly two meters from the previous one in the row.

_There? _It broadcast.

Trinity looked down at the screen of her tiny handheld and shook her head. Though the sentinels could not speak, they had set up a sort of wireless internet and communicated with the humans through receiving devices which translated the signal into text.

"No," said Trinity, attempting to keep the exasperation out of her voice. After a year she was still amazed at how slow the machines were to catch on.

The sentinel ruffled its tentacles, looking for a moment like a fluffed up bird. A sign of irritation, Trinity had learned.

Or how stubborn, she amended silently. Though it was still believed to be impossible, the machines behaved for all the world as though they were capable of emotion.

"Not there," she insisted. "Trees in a forest grow at random, not in perfect geometric shapes."

She had been telling the worker sentinels this for weeks, and yet the foliage in the greenhouse so far was in such perfect rows a giant could have played a game of Boxes with it. Even when the sentinels did appear to plant something out of formation, they just filled in the gaps later, completing the perfect pattern.

Trinity sat on the ground to watch the sentinel work. The idea was to repopulate the Earth's surface with plant life in carefully temperature controlled greenhouses. The machines were working on an artificial ozone layer, and when the time was right, they would remove the glass from strategic locations, thus rebuilding the atmosphere. As conditions improved, the plan was to phase out the Matrix slowly, so that the people would never know.

Trinity sighed and brushed a hand across her eyes as the sentinel kicked up a wad of dirt that just _happened _to hit her in the face. She knew she would not see the full deletion of the Matrix and return to surface dwelling in her lifetime. It was a sobering thought. Early euphoria at the war's end had faded fast, replaced almost instantly by grief and an overwhelming exhaustion since—

She pushed the thought from her mind and stood up as she realized that the sentinel had finished planting the tree…and that it had formed a perfect right triangle with the ends of the two rows. Trinity brushed that damned piece of hair out of her eyes for what seemed like the millionth time and bit the inside of her lower lip to keep from screaming in exasperation.

* * *

The camp of dwellings had been slapped together quickly, much like the mud huts of the Indians, centuries gone by. They were constructed mainly of plexiglass, windows everywhere to trap any rare heat from the sun. The greenhouses on other parts of the surface had been growing for several months now, managing to produce a scanty supply of fruits, vegetables, and cotton for clothing. It was not much, but the population was so small that it provided a noticeable supplement to what was already being produced in the Zion groweries.

Trinity stood in front of the largest window in the small foyer, watching the already dark sky fade to inky black. The ridiculous wish to see the moon, or even a beam of silvery light tugged at her heart. She shook her head at herself and pinched the bridge of her nose with one hand. The sound of laughter in the other room floated through the corridor, echoing a little. They must be eating dinner, she realized, but did not move. She had no wish to join the others. No wish to see any of them ever again.

"Surface duty again? I'd been wondering where you were."

Trinity jumped slightly, then forced herself to take a deep breath and turn around slowly. Niobe stood in the dimming lights, lounging against the wall and regarding her with a slightly raised eyebrow.

"I like it up here," said Trinity simply.

Niobe narrowed her eyes and took a step closer, straightening to her full height.

"Bullshit. Nobody likes working up here in this wasteland."

Trinity shrugged, still trying to keep her face neutral.

"Better than down there, at least."

"You don't really believe that."

Trinity laughed bitterly and turned back toward the window. It was so dark the clear sheet looked like a solid wall of blackness.

"Funny how everyone wants to tell me what I believe lately."

"Trin—"

"Don't call me that."

Niobe sighed.

"The people don't know any better. No one wants to tell the truth anymore, it's all rumors. They just—"

"They blame me. I know."

"Trinity, you can't look at it like that. No one's being reasonable about this." Niobe shook her head. "An entire damn year and no one can be reasonable."

Trinity turned and leaned against the wall, cringing as the muscles in her back protested.

"It's perfectly reasonable. They can't accept it. They needed someone to blame and so they blamed me. And now it's been a year. Who would bother to apologize?" She shifted uncomfortably, eyes on the floor. "And it _was_ partly my fault."

"Trinity, you're too damn hard on yourself. You did everything you could. You're damn lucky to be alive yourself. And it's not like there isn't any hope at all…the Zion medical staff said Neo was improving when I left. That his neural patterns were more active."

"Niobe, they've been saying that for months. He's been in a coma for a year. They just…don't want to stop hoping any more than I do."

Niobe made her way over to the window but kept her distance. Trinity watched out of the corner of her eye, refusing to turn. She had always liked Niobe; when Trinity had first been unplugged, it had been Niobe that taught her to live in the Real World, showing her everything Morpheus could not offer to a sixteen year old girl. Niobe cleared her throat at last, jarring Trinity from her thoughts.

"Come on. You need to eat. You're too thin as it is."

Trinity attempted a sneer, but failed miserably.

"Yes, Mom."

Niobe laughed a little and started off toward the mess hall.

"Good to know you still have a sense of humor buried under that ice exterior."

Ghost and Link looked up at the sound of the door opening; they were the only ones still left seated at the long table. It was late even for dinner.

"So what is it tonight, boys?" asked Niobe, taking a seat at the table across from Link.

Ghost ladled up a spoonful of whatever was in his bowl and let it run back in slowly. It was green. And very lumpy.

"Cream of…something that was apparently left over from the planting," said Link, wincing.

Ghost went over to the wall spigot that served as their food supply and filled another bowl with the green stuff. He held it out like an offering.

"Trinity?"

She shook her head silently, which earned her a glare from Niobe. She opened her mouth to protest, but was interrupted by the door being flung open and slamming against the wall. Kid dashed in, his face flushed in the perpetual excitement that had at last gotten on everyone's last nerve and caused him to be banished to surface duty.

"TRINITY!" he all but screamed.

She flinched visibly at the sound of his voice and turned to regard him with the icy glare she'd become famous for among the Resistance.

"Jesus," she snapped. "I'm _right here_, Kid. And if one more person says my name today, I'm registering for a new one. Getting overused."

"What?" said Kid, lost.

Trinity shook her head in exasperation.

"Nevermind. What is it?"

"Call for you."

"From?"

"Morpheus."

Kid beckoned for her to follow, and she obeyed, all but treading on his heels in her haste. He motioned to a phone on the table in the communications center, and she snatched it up.

"Morpheus?"

"Trinity, listen to me." The deep voice was filled with an urgency that made her heart speed up. "He's awake."

She just stood there for what felt like hours, frozen in shock. Her heart pounded in her temples, and the phone was suddenly so heavy she could barely hold it up.

"Trinity?"

"I'm here. I'm coming back."

"You haven't finished your shift on the surface. You have two more days before you're cleared to return."

Her free hand clenched in frustration, ripping the hem of her already threadbare shirt.

"Morpheus, don't do this to me—"

"I'm not doing it to you, Trinity. I'm doing this for you. He isn't ready yet."

"What the hell is that supposed to mean?"

"That you're going to have to be patient. Take these two days to prepare yourself. It isn't going to be easy for either one of you."

* * *

Review, please!


	3. Light

Author's Note: Okay, so it's not the most exciting chapter I've ever written. But poor Neo needed the info. You guys are gonna like the next chapter...I promise.

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CHAPTER 2

_Bright white light.__ Hot. Burning. Like lightning slicing through charcoal clouds on a summer afternoon. Like the sparks flying out of a broken hose, scorching the deck. Like the blinding light streaming from behind those thousand pairs of sunglasses, shattering the darkness, filling the Matrix with the light of rebirth._

_It stung like a thousand needles, a hive full of wasps jabbing their stingers into his eyes. There was a voice somewhere in the room, screaming in agony. He winced at the sound, forced his hands up from his sides, clawing at his eyes trying to do something, anything to stop the feeling, but then there was someone else there, another pair of hands clamped around his wrists, forcing them down. Two more at his shoulders, pinning him to the ground, his head hitting something hard behind him as he attempted to struggle his way free. _

_Then just as suddenly, the light dimmed and the pain drained away to a dull ache._

Neo attempted to open his eyes again, cautiously this time. The sensation was strange, as though he could suddenly feel them there, too big for his head, grating against the backs of his eyelids. He winced. The world was a dim blur of colors and shapes and he wondered for a moment if he was still dreaming. Or better yet, dead. He could feel something warm on his arm, and he looked down to see a blur of redness. Blood. He swallowed, only to find that the inside of his throat was raw. The screaming voice had been his own.

"Welcome back."

The deep voice made Neo jump, and he turned toward it, though all he could make out was a dark form standing over him. It made him nervous.

"Back?" he forced through cracked lips. His own voice sounded alien.

"You're very lucky to be alive."

The words hit him like a tidal wave. He inhaled them, choked on them. This couldn't be real, couldn't be happening. He had wanted nothing more than to be finished with it all, done fighting at last. He wanted to rest, to let go of the tension that had been eating away at him for he couldn't even remember how long. Most of all, he wanted to be with her. Wherever she was now.

"Fuck lucky," he managed after a long moment.

"You don't want to be here?"

He recognized the voice now. Didn't know how it had taken him so long. _Morpheus._

"I…" Neo broke off as a fit of intense coughing took him by surprise. A pair of hands helped him sit up, bracing his back, held a plastic cup of water to his lips. He felt sick with shame at the need for help with such simple tasks.

"Where am I?" he managed at last.

"The Zion medical center," said Morpheus' voice.

Neo finished with the water and attempted to set the cup on the bedside table, only to discover that he could not reach far enough. He winced at the sound of the empty plastic cup bouncing flimsily along the floor.

The Zion medical center was nothing like the rest of the city, he knew. He had been here enough times to memorize the sight of it, though not a single feature was clear enough to look familiar to him now. Whereas the rest of the city was built by simply reinforcing the natural rock formations with steel, the medical center was more comfortably furnished. The floors actually were carpeted, the heating was more intense there, the food better. It was the one place where people could go to get away from the grit and hard reality of life.

"How…I remember…the crash…and Smith…and then…"

"It would seem that the machines are capable of gratitude after all," said Morpheus darkly. "After the battle ended and peace terms negotiated, you and Trinity were escorted back in a sort of makeshift shuttle by the sentinels. Gave people here quite a scare. When you didn't recover right away, some said that you'd sold your soul to the machines in order to save our city."

"Trinity?" he asked, barely daring to hope. "She's alive?"

"Yes," said Morpheus slowly. "Moreso than you've been yourself until now."

Neo was floored by the news. He'd been forced to relive the crash so many times in fewer dreams it was permanently burned into his eyes, haunting him night and day. It was all so real he had been sure that it had been exactly as his nightmare vision saw. But then, he had learned a long time ago not to make assumptions. Perhaps it wasn't really real after all.

"Where is she?" He forced his voice to remain calm, though his mind was suddenly reeling with questions. If she was really all right, he couldn't believe that she would not be here.

"On the surface," said Morpheus cryptically. "She's been…she's done more tan her share of organizing he surface reconstruction teams up there. There's a lot for you to be told when you're feeling better."

Neo sat in silence for a moment, trying to downplay the fact in his own mind. There was something not right about the way Morpheus had said that. If she was doing more than her share of surface work, then it must be her choice. Which meant that she had chosen to be up there rather than in Zion. He suppressed a twinge of jealousy at the thought of her moving on. But then he supposed it was only natural if—He brushed the thought away, dismissing it as ridiculous.

"You have to understand, Neo," said Morpheus as though reading his thoughts, "this hasn't exactly been easy for her either. The first few weeks, she stayed down here, almost never left you. But then weeks became months, and there was still no sign that you were going to recover. And people started to talk. They thought it was strange that she recovered and you did not. There were threats made. I advised her to take a job on the surface and stay there as long as possible as much as possible."

"They blame Trinity?" asked Neo, shocked. The people could be demanding in their expectations at times, yes, but they had always been supportive. But then, if it had been long enough, he supposed…

"How long has…have I been…here?" he managed, pressing one hand to his temples. He was rapidly developing a raging headache.

"It is almost a year since the war ended," said Morpheus with that same not-quite-revealing tone.

"A year…"

"Rest, Neo," said Morpheus, pushing him back against the bed. "You can move back to your apartment in a few days. They want to keep you a few more days for observation. And to work on your eyes."

"My eyes?" asked Neo, already half asleep.

"They're going to try several more operations. The doctors are hopeful that you could possibly regain your sight completely. The machines appear to have attempted to restore it, but they were not able to succeed entirely."

"Wait…I don't understand…a year?"

"Rest, Neo," he repeated. "I've sent word to Trinity. She'll be here in a couple of days."

* * *


	4. Homecoming

Author's Note: So, did I scare people with that last chapter, or are you all just as busy as I am? Anyway, I hope you'll like this one better. I promise that this story actually does have a plot, and it's not all "let's be happy and make it all better!" either. Those fics make me cringe. Happy Valentine's Day (yeah, right), and I hope you enjoy.

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CHAPTER 3 

She reached the familiar domed doorway and paused, feeling suddenly awkward and shy. She knew the code, but barging in seemed rude all of a sudden. Presumptuous. Trinity raised one hand to knock, then hesitated again, not wanting to disturb him if he was asleep. She let her hand drop limply back to her side and just stood there for a moment feeling utterly ridiculous. A year ago she had fought her way through Hel at gunpoint to get Neo back, and yet now she stood paralyzed in fear at the thought of knocking on his door. Just then the door creaked, making Trinity jump, and swung open to reveal Morpheus. He smiled that unnervingly knowing smile at her and gestured for her to take a step closer.

"I had a feeling you'd be here soon."

"I—" Trinity shook herself. "I got here as fast as I could. Is he—"

Morpheus nodded, holding up a hand for silence.

"Awake and all too alert. He's been asking for you."

Trinity managed a weak smile at that despite herself.

"So should I…" she trailed off, gesturing toward the door.

"Yes. I'm going to leave you two to yourselves." He took several steps past her, then turned back. "But Trinity…try to stay calm. He needs you to be strong right now. And stick to the candles, his eyes can't take anything brighter yet."

With that, he turned and strode off down the corridor without so much as a goodbye.

Trinity sighed, forced herself to take a deep breath, then punched in the code. She closed the door slowly, painstakingly making sure it didn't creak or slam. The room before her was almost unrecognizable, aglow with the light of what must have been twenty or thirty candles.

_Like the whole thing was built with light…_

She shuddered and forced the thought aside, making her way over to the bed. He was lying on his side, propped up on one elbow, watching her silently. His pupils were huge in the dim light and for a moment she wondered if he could see her.

"Hey," she said at last, lamely.

Neo's entire face bloomed into a rare smile at that single word.

"Hey."

He shifted closer to the wall, making room for her. Trinity sat on the side of the bed and took his hand in both of hers, pressing it palm-up to her lips.

"How are you feeling?" she asked after a moment, still shy despite herself.

Neo pulled his hand free and brought it down to rest on her thigh, fingers playing idly along a wrinkle in her pants.

"Tired," he answered finally. "And more than a bit useless."

Trinity nodded silently, running a hand across his forehead, brushing back dark bangs. He shivered slightly under her touch and she pulled back a little, uncertain.

"Can you see?"

Neo sighed, an expression of utter frustration creeping over his features.

"yes, but not well. The doctors…they claim it'll get better over time." He laughed a little, darkly. "I can't decide which is worse, to not be able to see anything, or to see only a blur of colors."

"This is better," Trinity answered hastily. "I've missed your eyes."

Neo shook his head.

"I wish I could see yours."

"You will."

Neo sighed again, louder this time, and rolled over onto his back, scrubbing at his face with his hands.

"I'm so sorry, Trin," he said after a moment, his voice slightly muffled. "I shouldn't be doing this to you. Especially not now."

Trinity swallowed hard against the painful tightness in her throat, fighting for control.

"Don't be," she managed after a moment. "Don't ever be sorry."

He rolled over again, his back to her now, face still buried in his hands. She could see his shoulders shaking slightly.

"Neo…is there anything I can do?"

"Hold me, Trinity."

His voice was weak, broken. It was almost more than she could bear. She wrestled off her boots and crawled into bed beside him, wrapping her arms around his waist and resting her cheek in the space between his shoulder blades, breathing in his scent.

He pulled away after a moment and rolled over, taking her in his arms. His lips trailed kisses along her chest and collarbone, hands exploring her body.

"Your hair," he whispered after a moment, breathless.

Trinity laughed at his surprise, the feeling bubbling in her stomach like an alcohol buzz.

"Yes."

"I thought you hated it long."

Trinity shrugged and slipped one leg up over his waist. She could feel his ribs pressing into her side. He'd lost an alarming amount of weight.

"I decided it was time for something different."

Neo smiled a little and ran his fingers through it.

"I like it. I think."

They were silent for a moment then, and the tension crept back into his face.

"What is it?" asked Trinity, resting one hand along his jaw.

Neo shook his head.

"It's just…I don't …Why did they bring me back, Trin?"

She sighed.

"I don't know. I don't think we'll ever know." She paused for a moment, trying to get up the courage to ask him the next question. "Are you glad they did?"

"I don't know. I guess I should feel grateful, right?"

"I don't care what you _should _feel, Neo. Only what you _do _feel. When they brought me back I was so angry….a part of me thought they did it as their last little attempt at making us all miserable. I just…I'm so tired of everything hurting." She regretted it the instant she'd said it, Morpheus' words echoing in her mind, but Neo didn't seem upset by it.

"I just don't know what I'm supposed to do now," he said softly. "The war is over. I never thought beyond the end of it. The only place I really have any power is in the Matrix, and there's no reason for anyone to jack in now. And here…well, I'm just another guy. Hell, not eve. I'm a guy who's a social failure."

"Neo." Trinity found his hand under the covers and squeezed it tightly. "You've spent so long living for everyone else. I know it's hard. But you're going to have to learn to live for yourself."

He nodded a little, still not completely convinced.

"I know…it's just…before I knew I was making a difference…now…well, it's almost like…before."

Trinity pushed lightly on his shoulder until he rolled onto his back. She leaned over, one arm on either side of him, lips just inches away from his.

"For what it's worth," she said softly, "I don't give a damn about wars or prophecies. You are, and always will be the one I love."

Neo cupped one hand against the back of her neck, then leaned up and kissed her. The sudden contact hit her like a wall, shattering all remnants of control. She pulled away, but not fast enough, desperately trying to salvage her calm. Neo wrapped his arms around her with surprising strength, pulling her on top of him.

"Trinity…you're crying." His voice was strangely filled with wonder.

She had never cried in front of him. Never.

She swiped roughly at her eyes, angry at her own weakness.

"Thought you couldn't see," she choked, burying her face against his shoulder.

"I love you, Trin," he whispered into her hair. "I'm sorry it has to hurt so damn much."

"Don't," she murmured. "Just stop apologizing. But jesus, I missed you, Neo."

She shifted her weight off of him, and he leaned over and kissed her again. After a long time he pulled away and wrapped his arms around her, rubbing his thumbs across her back in rhythmic little circles. She was almost asleep when he spoke again.

"Trinity?"

"Yeah?"

"We made it."

"You said we would."

* * *

Review please! 


	5. Patient Zero

CHAPTER 4

"Ready?" called Trinity from the small bathroom. She wasn't entirely sure why she was bothering with her appearance, but it was the first time she'd gone to any public gathering in Zion since the end of the war, and she didn't want to give the people any more reason for slander. She poked her head out of the bathroom to find Neo still sitting on the bed in his pajamas. She sighed and took one last glance in the mirror. She had never once felt beautiful, though every man she'd ever met insisted on telling her that she was. The gray top she'd opted for looked strangely light after a year of only black and dark blue, but she'd decided it was time to end mourning. It was the first time she'd seen her hair loose since she'd let it grow, and suddenly she wondered if the people would even recognize her. Better, perhaps, if they didn't.

Trinity stepped out of the bathroom and made her way over to Neo, resting her hands on his shoulders. He turned toward her instinctively, though she knew he couldn't really see her face.

"Neo…they're expecting us."

He nodded again, more slowly this time, but didn't move.

The party was being thrown partially to celebrate the one-year anniversary of the war's end, and partially to celebrate Neo's recovery. It promised to be horrendous.

"Neo…"

"I'm not going," he muttered at last, so softly she wondered for a moment if she'd really heard.

Trinity sighed and sat down beside him. In the weeks following his recovery, he'd been plagued by a constant stream of questions and demands both from the council and from people who still expected him to lead. He had no answers for any of them, had no idea how to go forward now that the prophecy had been fulfilled, and no one could simply accept this. They all insisted on believing that he was holding back some secret wisdom. Neo had responded by rapidly becoming a recluse, holding back even from her. He'd stopped eating, stopped sleeping, spend most of his time simply staring straight ahead, unseeing.

"Neo, you have to." She grabbed his hand and squeezed it between both of hers. "They're never going to change if you don't prove them wrong."

He laughed bitterly.

"Prove what, Trinity? That I have nothing to offer them? That I'm a fraud?"

She leaned in to kiss his neck, but he pulled away roughly, as if he'd been slapped.

"Neo…you know I didn't mean it like that. You're not a fraud. We just…don't know what you are yet."

Neo rolled his eyes at her, and she shuttered at the strangeness of the gesture. It was so utterly familiar, so much so that she had to keep reminding herself he could not really see. He sighed.

"I just…this is going to sound strange."

Trinity laughed.

"You think after fifteen years working for Morpheus you can weird me out? Go ahead and try, flyboy."

"At first I didn't even want to have the responsibility…but then…as things started falling into place it got to be…I don't know, exhilarating. I'm not used to having people listen to me. Notice me. Respect me. I'd never felt like I could make a difference before. Like I could matter. I told myself it wasn't about the fame, and mostly it wasn't, but now…now I don't know if I can go back to being Mr. Anderson, the hacker geek who lives alone."

"Neo…" She leaned over and wrapped her arms around his shoulders, ignoring him when he tried to pull away. "I understand, it's natural that this isn't going to be easy. But no one is asking you to go back to where you were before. I don't care how hard you push. I'm not leaving. So you'd better learn to live with it."

He'd stopped struggling midway through her reprimand and buried his face in her shoulder, leaning into her and wrapping strong arms around her waist.

"Shit, Trinity, you'd better not leave me. Then I'd really be nothing…" He turned his head against her and kissed her gently. "I'm sorry I've been so distant. I just…don't know who I am anymore."

"Maybe I don't either." She leaned over, kissed his forehead, then ran one hand through his tousled hair before pulling away. "Come on. Get dressed. We're already late."

"I'm not…I can't…"

"Please, Neo. Go for me."

He sighed and brushed his hands over his face, exhaling slowly before he answered.

"All right. For you."

* * *

Parties in Zion always followed one of two formats. The first was a loud communal gathering of the entire city which included loud music, plenty of alcohol, and very few inhibitions. The second was a selective formal party of the council members and their guests of honor featuring formal dress, a quiet dinner, and much stuffy conversation. This particular gathering followed the first format.

The party was already in full swing when Neo arrived, Trinity on his heels as if to make sure he wasn't going to make a run for it. Though he knew he should be annoyed, he was grateful for her presence—he didn't entirely trust himself not to flee for his life when he stepped into the main cavern and was immediately bombarded by the guttural pulsing of the drums and an overwhelming smell of sweat. He'd never liked social gatherings, and parties that required dancing were even worse, especially now that he didn't have the luxury of being able to navigate through the crowd on his own. He'd been using a small white cane to walk since his release from the hospital wing. It was effective, but utterly humiliating. He jumped a little at Trinity's hand on his back.

"You okay?"

Neo shivered a little at the feeling of her breath on his neck. He leaned over to whisper in her ear.

"Yeah, I guess. I just…what's going on?"

"People are getting drunk and dancing. More or less like last year. I don't think anyone's noticed us yet. Most people are…otherwise occupied."

Neo nodded and took a step forward, then realized the cane would be utterly useless in such a rowdy crowd. He leaned it against what felt like one of the pillars and turned back to Trinity.

"Help me?" He hated himself for having to ask, but he knew he had no choice.

"Of course." She was at his side instantly, one hand on his back, the other on his arm. "Morpheus and Link are about twenty feet away at two o'clock. It's not too crowded between here and there, just trust me."

The first few steps were harrowing and awkward, though he knew she would not let him fall. Walking without sight was singularly strange; he felt off-balance even on flat surfaces, as if the bottoms of his feet were uneven and could pitch him forward at any moment. The partial sight only served to make his sense of balance worse, phantom obstacles perpetually at the edge of his vision, threatening a collision at any moment.

"Well, if it isn't our guests of honor," said Morpheus' voice a few moments after they'd come to a stop. "Shall I tell people you've arrived?"

"Please don't," said Neo uncomfortably. He'd always had a hard time looking people in the eye before, but now it was unnerving not to be able to see expressions.

"Neo, good to see you, man." Link. A warm hand shook his. He shifted as Trinity pulled away, presumably to greet Link herself.

"Same to you," said Neo, then added uncomfortably, "or I suppose I should say 'hear you.'" The joke was tense and unfunny, and fell awkwardly to the ground.

"So," said Link, breaking the silence at last, "I hear Kid is going to be attending the Academy at last."

"The Academy?" said Trinity incredulously, "I thought they shut it down."

"No," said Morpheus. "There was talk of it, but the Council decided to keep it open in order to train more overseers for the surface reconstruction."

Trinity laughed.

"A far cry from combat training. Hope he won't be too terribly disappointed."

Link started to say something else, but was interrupted by the sound of a rough cry ringing out over the music. It was a strange sound, different from the reveling calls of the celebrating Zionites. This sound was raw and inhuman, something between animal and the supernatural. It came again a few seconds later, and then again, louder. The music stopped after the third cry, and sounds of a struggle could be heard over the sudden silence. Neo felt his blood run cold, and found himself groping for Trinity's hand.

"What's happening?"

"I don't know." Her voice was tight with something, perhaps anger, perhaps fear. "It looks like a fight of some kind. Or an overdose. There's a couple people on the ground, and a big clump standing around looking down at them."

"Trinity." It was Morpheus' voice again.

"Stay here," she whispered against Neo's neck. And then she was gone.

Neo stood in the midst of the chaos, one hand braced on the rock wall. There was shouting, and people moving all around, and then—

_The Chateau, on the back patio, staring out at the mountains.__ It was cold up here, though it had not been before. The glare off the snow was harsh, and he did not have his usual dark sunglasses. The glare and the sudden crisp image were a shock to his system, and he stood reeling, unable to get his bearings. He jumped at the sound of footsteps behind him._

_"Hello, Neo."_

_He turned to see the Architect standing on the patio, grinning that cool, cruel grin of his._

_"You've gotten farther than any of your predecessors, Neo. But not far enough." The Architect laughed. "You will never make it far enough."_

_Neo shook his head, turned to run. He had to get away from this place, anywhere, anything would be better. This couldn't be happening, and yet—_

"Neo!"

A pair of hands, shaking him by the shoulders.

"Neo, talk to me."

"Yeah," he gasped, recognizing Trinity's voice.

"What happened?"

"Nothing," he lied, not ready to face it yet. "I just…got disoriented. What's going on?"

There was a long pause before she answered.

"Two people were…apparently overwhelmed by the party. They had a bit of a reaction, a kind of fit, I guess you'd call it. They uh…came down with some kind off illness. There were pustules all over their faces and necks, and it looked like…it looked like plugs were trying to come through their skin."

"Plugs? On native Zionites?"

"That's what it looked like. I…I couldn't tell. I guess…I guess I must be wrong."

Neo knew by the sound of her voice that she was not wrong. She hardly ever sounded scared, but when she did it was never without reason. He tried to force the words to the back of his mind, but they just kept repeating, over and over like a broken record.

_You will never make it far enough…_

* * *

Review please!


	6. Duty

A/N: Sorry this took so long, but I'm in the last few weeks of rehearsals for my show, and I'm really sick. Hope you guys are still reading. Space Between should be updated this afternoon too, so look for that.

* * *

CHAPTER 5: Duty

Neo was already awake when the knock came, though it was the middle of the night. He hardly slept anymore, was still haunted by nightmares, though he wanted nothing more than to slip into the dark oblivion of sleep, it would not come. At first he thought he'd imagined the sound, that the pounding on the door was really the pounding in his head, but then it grew louder.

"Neo? Trinity!" The voice was Link's, and filled with desperation.

Neo sat bolt upright, pulling himself away from Trinity who was still asleep, exhausted by the day's events. He swung his legs over the side of the bed and attempted to make it to the door without waking her, but he somehow got off track and bumped into a chair, knocking it over with a crash. His left knee instantly sang with needles of pain.

"Neo?" It was Trinity's voice, filled with concern. "Neo, are you all right?"

"Yeah," he managed, gingerly feeling his knee. Bruised, he decided, no worse. "Door, Trin."

The light went on, but it made little difference. Things had gotten somewhat clearer, he decided, though it was still little more than nondescript shapes. He felt Trinity brush past him, and heard the door creak open a moment later.

"What is it, Link? What's wrong?"

Neo picked the chair and found his cane by the side of the bed before making his way over to Trinity.

"It's Morpheus," he heard Link say.

"Oh, jesus…is it bad?"

"Like the others…it's like…it's like he's jacked in and can't get out. The Council's called an emergency meeting."

"When?" asked Neo.

"Now."

It was only a short walk through the dark tunnels of the city to the Council chamber. Neo had been there so many times at this point that he had nearly memorized the way, but it was still hard to navigate the uneven floors. His heart sped up as they neared the door; coming here never meant good news.

Trinity grabbed his arm and led him up the stepped risers that lined one wall of the council chamber. Neo managed to stumble up several rows before settling beside her. She slid in closer than was truly necessary, but he wasn't about to complain.

"It has now been nearly three weeks since the discovery of this…virus…in Patient Zero. Since then, there have been nearly one hundred instances in both pod-borns and native Zionites." Councilor Hamann sounded flustered. "And now Morpheus, one of our very best, has fallen ill as well. Because of the apparent virility of this new threat, and our inability to treat it, the Council requests that a ship be sent to the machine city to see if they are behind the cause of this."

There was a pause as the Council members discussed something in further detail. Neo leaned forward, attempting to hear, but the acoustics of the room were bad and they were simply too far away for him to make any kind of sense out of it.

"Ordinarily," Councilor Hamann resumed, "I would send Captain Morpheus, since he is our most experienced captain. However, due to his recent illness, that will not be possible. And in the aftermath of the war…the Council thought it would be wise to create an entirely new ship and crew. Trinity."

Neo felt her tense beside him, then stand up. He shuddered at the Councilor's words and crossed his arms over his chest.

"The Council asks that you accept a promotion, and become captain of an entirely new ship, the _Athena_. Your mission is to make contact with the machines in their city. It is up to you to choose a crew for your ship if you accept."

Neo bit his lip and clenched his fists still crossed under his arms. A wave of dread swept over him, like a ton of lead. Images from his nightmares swam in the depths of his mind.

_No, no, can't go back there…not again…not when…_

"All right."

The words hit him like a ton of bricks, shattering the calm he'd been working to build up over the past few weeks.

* * *

"I'm ready, Trin."

Trinity sighed and looked up from the pile of clothes she was attempting to fit into a very small duffel bag. He was standing by the bed, a duffel bag slung over one shoulder, his cane in his other hand. She forced herself to take a deep breath and let it out slowly.

"Neo, you're not going."

He looked like he'd just been slapped. He slowly lowered the duffel bag to the floor and sank down onto the bed.

"Trinity…"

"You're not. I can't let you. Not after…everything."

Neo stood up and came over to her, walking with surprising ease. He took her by the shoulders and fixed her with those dark eyes. She shifted uncomfortably under his scrutiny.

"Trinity, I can't let _you_ go back there alone. It's too hard…not knowing…I couldn't take…losing you again." His voice still had that weak, broken sound to it.

"Neo, you're not going to lose me. There's nothing dangerous about this mission. But I'm not…I can't let you go." As soon as the words were out of her mouth she realized how unconvincing they sounded.

He sighed and went back over to the bed, sitting down hard and crossing his arms over his chest. He was irritated. Trinity followed him over and attempted to put a hand on his shoulder, but he pulled away roughly.

"So I'm not good enough for this mission but you are? Look, Trin, I know the majority of this city thinks I'm useless, but you…"

"Neo, that's not what this is about and you know it," she snapped, the words coming more harshly than she'd intended. "This is my duty, you know that. I have to accept this mission. It's why I'm here."

"Is it?" he asked softly. "Or do you just want to get away from Zion? Away from your new life…pretend you're still someone."

"Neo!" The words were like a punch in the stomach.

"What, Trinity? You think this is easy for me, letting you go off like this?"

"Neo, you're not _letting _me do anything. It's my choice. I don't belong to you, you know."

She regretted it the instant the words were out of her mouth, but she was too angry to apologize. An awkward silence fell, then, neither one of them wanting to worsen the damage.

"I see you die," he whispered at last, his voice barely audible.

"What?"

"Every time I close my eyes, every time I fall asleep, I see…" he trailed off, voice breaking noticeably.

"Oh, jesus, Neo." Trinity sat down beside him on the bed, his words turning her legs to rubber.

He turned suddenly and pulled her into a crushing hug.

"I can't do this, Trin. I can't…say goodbye."

She sighed again, then kissed him gently.

"God damn it, Neo…come with me…who am I kidding."

He offered her a weak smile, then stood up, shouldering his duffel bag again.

"All right then, let's go see this new ship…_captain_."

* * *

Review please, cuz I'm sick and it'll make me feel better! 


	7. The Rubik's Cube

Author's Note: As I said in my note for Space Between, I might not be updating for a couple of weeks due to my show being in its final weeks of rehearsal and performance. Please don't think I'm abandoning it.

* * *

Chapter 6: The Rubik's Cube 

"Oh my god…_this _is our ship?" Kid stood on the launch pad, staring wide-eyed at the _Athena_. It was larger than most of the former Resistance fleet, cobbled together from pieces of retired ships, including what had been salvaged from the Nebuchadnezzar.

"Her ship," corrected Neo, taking a step closer to Trinity.

"Come on now, I know how to share," said Trinity, grinning. The circumstances of the mission were far from ideal, but she had secretly wanted a ship of her own since she had first been brought aboard a Resistance vessel. She wasn't entirely sure why she'd allowed Kid to be the rookie on her ship, but the look on his face when he'd approached her the night before was so full of disappointment that he would never have a chance to serve that she simply could not refuse. Besides which, despite his tendency to be annoyingly happy, Kid had done everything possible in his own way to help her through the past year.

Trinity managed at last to tear her eyes away from the outside of her ship and turned to the rest of her crew. She had ended up with the very best group she could have imagined, though she was a little wary of how they might get along. Niobe had humbly agreed to act as first officer, though it meant temporarily giving up her rank. She had never been the kind of person to openly share her emotions, but it was obvious that Morpheus' sudden illness was taking a heavy toll on her. They had become more than close over the year since the war's end, though neither would speak about it to anyone. Ghost had insisted on coming with her, along with Sparks, who claimed he was going just to get out of Zion. Link had once again reluctantly signed on as operator, though he was wary as always.

"Come on guys, let's take a look at this girl." She started toward the ship, pausing at the entrance ramp to make sure Neo managed to get up it all right.

The inside of the _Athena_ was laid out like all other Resistance vessels, though it did not have quite the same cramped, enclosed feeling she'd grown accustomed to. The computers in the core were slightly updated, the viewscreens larger and the graphics clearer. The customary seven seats slightly larger than before. The lower deck seemed almost empty, as the ship had been outfitted with all the most efficient technology and no longer needed as many engine rooms.

"Holy shit…" gasped Kid, looking around.

"Careful," scolded Trinity. She was fully aware that with the crew she had Kid would be spouting profanities like a sailor from the Matrix within a matter of days, but she couldn't let it go without at least attempting to keep him on the right track.

Kid blushed, suddenly filled with respect.

"Yes, sir. Uhh…ma'am."

Trinity fixed him with an icy glare.

"Captain!" yelped Kid.

"Kid," she said slowly. "Do something for me."

"Yes, captain?"

"Go check the mess hall and make sure our food and water spigots work. Then go make sure everything in your cabin works. Above all, make sure I do not see you for at least the next hour."

"Yes, Captain!" said Kid, and ran off.

She smiled at Kid's retreating form. She knew she was being harsh wit him, but it would be necessary if she was to take this fidgety over-eager teenager and turn him into a useful officer aboard her ship. In a way he reminded her of Mouse, though she was not entirely sure that this was a good thing. The thought brought with it a pang of sadness, both at the memory of fallen comrades and the ever-present knowledge of Morpheus' condition, the entire reason for this mission.

"Shall we?" asked Niobe, jarring Trinity out of her thoughts and gesturing toward the cockpit.

Trinity nodded and led the way up the small ladder to the cockpit, leaving the others to their own devices. Sparks' voice echoed up through the hallway the minute they were out of the room, relating some tale of his masterful endeavors in a Zion bar to a very disinterested Ghost.

Niobe slipped into the copilot's chair, eyeing the controls greedily. Trinity sad beside her and began the customary preflight systems diagnostics, her heart beating a little faster as each green light flickered to life on the console.

"You know, I don't think I'll ever get tired to flying these things."

"I know the feeling. For years all I thought about was how soon I could get out of the fleet…now I realize how much I miss it." She checked the indicators on the control panel one more time, then turned back to Niobe. "All right. Let's see if this bird can fly."

Niobe picked up the intercom with one hand and strapped in with the other.

"All right, boys. Time to go. We don't want to be cleaning body parts off the new equipment once we're in the air, so strap down back there."

"Well with you flying…" came Sparks' voice up through the grated floor.

"You couldn't be in better hands," Trinity yelled back as the ship began to lift off the landing pad.

It rocked a little as it gained altitude—the low, tight passage through the gates was one of the hardest maneuvers a Resistance pilot was required to learn. The idea was to allow only the Resistance ships and nothing else in or out. The ships, however, flew smoothest at a good fast pace, and tended to tip and shake when forced to move slowly.

Trinity glanced over to make sure Niobe was doing all right with the controls, then punched in the com frequency.

"Zion Control, this is the _Athena_, requesting leave at Gate Four."

The voice that came back over the comlink was distinctly female, though it crackled with static.

"_Athena_, this is Zion Control. You are cleared for takeoff."

"Damn right," muttered Niobe. "They don't wanna open those doors I'll bust right through them."

Trinity smiled a little at that as the gates began to rise, the metal groaning loudly. Niobe never lost her spirit, no matter what. A small crowd was visible on the rear viewscreen as the _Athena_ glided through the iron gates, though Trinity could not tell if they were wellwishers or an angry mob. Regardless, the sight of them left a feeling of vague unease in the pit of her stomach.

"Should be smooth sailing now," muttered Niobe as the ship found a path in the middle of the main tunnel.

Trinity nodded and unbuckled her safety harness. She'd always hated the thing, it made her feel trapped, though she realized it was necessary in combat.

"You okay up here?" she asked Niobe, standing up. The sudden feeling of the deck vibrating beneath her feet took her by surprise, and she had to grab the back of the chair for balance

"Go check on the boys," said Niobe, smiling a little.

Trinity nodded and made her way to the ladder, keeping close to the wall.

She found the rest of the crew in the mess hall, gathered around Sparks, who was putting on a show as always. He had what appeared to be a brand new Rubik's cube, probably from one of the Zion shops. Since there was less worry about the need for supplies recently, the craftsmen had been focusing more on comfort and entertainment items than ever before. The cube was gorgeous, rubber and perfectly symmetrical, the colors hand painted.

"So," said Sparks, holding up the cube. "Who will be the one to scramble this?"

"Let Kid do it," suggested Link, "he's good at mixing things up."

"I am not!" yelped Kid, flushing red.

Trinity leaned back against the corner of the wall, watching them silently. Ghost raised an eyebrow at her slightly, but no one else seemed to notice her intrusion.

"Well, if no one ever mixes it up, we can't solve it, now can we?" said Sparks, attempting to goad them on.

"It will get scrambled eventually," said Ghost mysteriously.

"How do you figure that?" asked Sparks.

"The principle of entropy states that everything in nature is moving toward chaos. Therefore, even if someone were to scramble the cube and then solve it again, it would retain some of the chaos. It will never again be as ordered as it is now, and it is not as ordered now as it was five minutes ago."

"Well, shit, Ghost," said Sparks angrily. "Now no one's going to want to scramble it. They might jinx our entire mission the way you talk."

An uneasy silence fell over the room, no one wanting to be responsible, but everyone wanting to see it done.

"I'll do it," said Neo at last. There was an air of finality in his voice that somehow made the task at hand seem much more dire than a simple game. As he took the cube from Sparks and began to twist it, Trinity felt the knot of unease in her stomach tighten into all-out dread.

* * *

Review please! 


	8. Crystal Balls

Author's Note: All right, so I managed one update for you guys this week, not two. But it's a long one, and I'm hoping to have Space up sometime mid-next week. We'll see. I am working on it though. I have a full timeline for Greenhouse now, which is close to 35 chapters. So yay for that. Thanks once again to all my reviewers, and I hope you enjoy. Yes, this chapter is slightly silly...I figured I'd give them some comic relief before the storm. :ominous music plays:

* * *

Chapter 7: Crystal Balls

The _Athena_ handled like a dream. Niobe sat in the pilot's chair, her fingers just barely resting on the controls. The thing was practically on auto pilot. She knew she could call Ghost or Sparks to come and take over for her, but she preferred the quiet of the cockpit for the moment. Her thoughts wandered back to Zion, to Morpheus in the medical center. He was being kept in a quarantine ward separate from all the other patients when she'd visited him the night before leaving. His head had been covered in electrodes, a dozen pieces of equipment flashing strange looking symbols from screens clustered around his bed. They were watching his mind, Lock had explained, making sure there was no attempt from inside the Matrix to hack into his thoughts and extract the access codes to the Zion mainframe during one of his fits. Niobe hadn't bothered to ask what he intended to do if they did discover what they thought to be an attack.

"Don't jump."

Niobe shook herself and turned around to see Neo standing at the entrance to the cockpit, hand pressed lightly against the wall for guidance. He'd abandoned his attempts to walk with a cane within his first day aboard the ship, opting instead to follow the walls by touch. Niobe smiled a little though she knew he couldn't see. She'd begun to see Neo in an entirely new light during the last few days of the war, and had regretted not getting to know him better.

"Don't want your pilot taking you for an unexpected roller coaster ride?"

"Preferably not." He made his way over to the copilot's chair. "But I hear you give a damn good one when you want to."

Niobe smiled absently and turned back to the viewscreen for a moment.

"I never got to thank you," she said softly. "You saved us."

He shook his head, a familiar look of self-deprecation creeping over his face.

"I did what I had to do."

He was silent for a moment then, fingers toying with a loose thread at the hem of one sleeve.

"I'm sorry about the Logos," he said at last. "I should have told you…I wasn't expecting to bring her back."

Niobe waved away his apology, the gesture too familiar to forsake, though she knew it was lost on him.

"Don't think about it. You needed it. God knows we would've lost a hell of a lot more had it not been for you."

He turned back to her at that. There was undeniably something about his eyes, she thought, something intense and slightly unnerving. She felt suddenly that he could see straight through her, though she knew he was still, for all practical purposes, blind.

"If I had told you, would you still have let me take her?"

"I knew," she said, surprising herself. It was truth, though, she realized suddenly. "I didn't want to admit it to myself, but I knew. It's strange, getting so attached to a hunk of metal, but it's like—"

"It's like losing your home."

She was struck dumb by his perceptiveness. Until just recently she'd taken him as nothing more than another hotshot soldier. This was something she would have expected out of Morpheus or Ghost.

"I was wrong about you," she said at last. "You are not who I thought you were. And I'm sorry for that."

He shook his head again, cutting off her apology.

"Don't be. Isn't worth the effort."

Niobe sighed. She couldn't stand it when people refused to acknowledge their own worth.

"Hey, I let you apologize to me, it's only fair that I get my turn."

He laughed at that, a rare display of emotion. It seemed somehow to Niobe that everything he did was shadowed a little by guilt and grief.

"All right, fine. But you have to promise me something."

"What?"

"That you'll stop apologizing."

"All right…but you have to stop too."

"Fine." He chuckled and held out a hand to her. She reached out and shook it, surprised by the strength of his grasp.

He started to get up, then turned back.

"Niobe…what made you change your mind? Was it the Oracle?"

She sighed and looked down at the controls, absently making slight corrections to their course.

"You mean did I come back from her and suddenly decide that I'd been wrong all along and the prophecy was true after all?"

He nodded.

"No. I just…hate feeling helpless. And it was all I could do. Don't take it personally, but I never believed in the prophecy. Still don't know if I do."

Neo shrugged, surprising her with his lack of reaction.

"Tell you the truth, I don't know if I believe it either. Not anymore, anyway."

He got up and left without another word.

* * *

"Well, well, would you look at that," remarked Sparks, looking over Link's shoulder at the screen which fed into the Construct.

Link burst into laughter and shook his head.

"Looks like hard training to me."

Trinity stood at the top of the ladder and just observed for a moment, debating whether or not to go and interrupt her crew members. They were supposed to be overseeing Kid's training, but she had a feeling that even he would not be this entertaining in one of the Construct sparring programs. Still, she hated to kill their joy, it was so rare that they found pleasure in their work anymore.

"Shiiiiit!" exclaimed Sparks.

Trinity sighed and left her hiding place to see what was going on as they broke into a fresh round of raucous laughter.

"Having fun, boys?"

Link's head shot around, his eyes huge.

"Captain!"

Trinity flinched; the title was still unfamiliar, and she wasn't sure she liked the looks of anxious respect the other crewmembers now regarded her with. The responsibility was like a deadweight in her stomach. The days of easy companionship were long gone.

"You might want to take a look at this," said Sparks, feigning seriousness as he gestured to the monitor.

She sighed and bent over the back of his chair, slightly unsettled by the appraising gaze Sparks was giving her. The last thing she needed was another suitor on her heels.

Kid was in the Construct, supposedly practicing his newly-uploaded combat skills. Instead, he had loaded a simulation of a Hawaiian resort and was currently lounging by the pool. He had on garishly flowered swim-trunks and sunglasses. In his hand was a glass of bright pink liquid complete with a little umbrella. In the water, clad in a scanty red bikini, was one of Mouse's blondes.

"God…" muttered Trinity. She had the sudden impulse to throw something at Kid's unconscious body in his chair, but she knew it would do her no good.

"Should I pull him out, captain?" asked Link.

Trinity pondered this for a moment, then shook her head, an idea rapidly forming in her mind.

"No." She went over to her chair and began punching in the familiar sequence.

"Captain?"

"Send me in, Link."

Sparks' eyebrows shot up, but he came over to help her into the chair anyway.

"Yes, captain," said Link, turning back to his screen.

"And Link?"

"Yes captain?"

"For God's sake, stop calling me that!"

* * *

Kid did not notice her immediately. In fact, Trinity very much doubted that he would have noticed her at all, had she simply remained standing and watching. He was far too busy with the pretty blonde in the red bikini. Trinity quietly made her way over to the back of Kid's lounge chair and leaned on it, clearing her throat. He jumped visibly, and emitted a sound like air being let out of a balloon.

"Captain!"

"Kid." She regarded him with an icy stare. He appeared to shrink under her scrutiny.

"I um…"

"I was under the impression that you had scheduled a training session in here."

"Yes ma'am."

"Then what, may I ask," she moved her hand in a wide, sweeping gesture around the resort, "is this?"

"I um…I…" His eyes lit up as a story came to him. Trinity groaned inwardly; she could practically taste the lie forming. "I thought you might be coming, and I've been doing some aquatic combat training, and so I thought that I would…um…show you."

"You just thought that I might be coming? How did you know?"

"I don't know…I just…had a feeling. I have this thing sometimes, where I can sense what other people are going to do. It's like I have um…"

"You have what?" asked Trinity, slightly amused despite herself.

"Crystal balls," said the woman in red suddenly. "He has crystal balls."

"Yes," said Kid, nodding enthusiastically, as oblivious to what he was saying as the woman.

Trinity bit her lip, caught between laughter and disgust. This was just the kind of woman she'd always hated, hadn't been able to stand as a girl. She had never understood Mouse's fascination with his creations, but she figured it was just as well that he'd programmed them not to be very vocal.

"Right. So then I'm assuming that if you used your uncanny intuition to foresee my coming and checking up on you…that you now have sufficient…crystal balls…to show me some of this aquatic combat?"

"Um…I…uh…" stammered Kid.

"Aw, come on, be a hero for me," crooned the woman in red.

Kid gulped visibly, bony adam's apple bobbing, and got up out of the chair. Trinity took a couple of steps back and pointed at Kid's sunglasses.

"You might want to take those off first."

"Oh! Right." He scrambled for them, fingers visibly shaking. For just a moment, she felt almost sorry for him.

"Go ahead."

Kid nodded, looking from side to side as though searching for an escape. The woman had come over to the side of the pool and was now leaning over sickeningly, displaying an obscene amount of cleavage and grinning like she'd lost a few chains of code somewhere along the way.

"We um…we should start…out here, so I can show you my normal combat first."

"All right."

Kid stood staring at her for a moment, then bent ever so slightly at the waist, as though afraid she'd ambush him if he bowed in earnest. Trinity mirrored him, then stood back, arms relaxed at her sides. This would be a show for her.

He took a deep breath, then came barreling at her with all his might. Trinity waited until she could barely feel the simulated wind from his running on her face, then threw herself neatly to the side. Kid was moving too fast to stop, and narrowly avoided a collision with the wall. The sound of giggling from the pool made a sick kind of soundtrack.

_Kid's theme_, thought Trinity, smiling a little to herself.

As he struggled to regain his balance, she hooked one hand under his arm and swung him around, administering a neat blow to his chin. Kid yelped and stumbled back, falling into one of the chairs.

"Come on, Kid." She gestured for him to get up. "I've told you this before. You can upload the moves, but you still have to learn to use them."

He picked himself back up gave her an insolent look.

"What are you doing to the simulation? I thought we could fly in here."

"Nothing," she said simply. "You can. But you have to believe it."

"All right," he said skeptically. "Let's try this again."

He jumped in place a few times, experimentally. His feet never got more than two feet off the ground.

"Damn!"

"Kid…"

"Yes ma'am!"

He charged at her again, using the same tactic as before. This time she kicked out as he ran by, tripping him. He managed to roll, though, and was back on his feet in a matter of seconds. Trinity let him connect this time, blocking his hits almost automatically. She let this continue for a few minutes, then grabbed him by the shoulders, pinning his arms to his sides, and pushed him backwards. He lost his footing as she had intended and plunged down into the deep end of the large blue swimming pool.

He came to the surface sputtering and spitting water, reminding her of a newly-unplugged in the power plants. The woman in red giggled louder.

"My hero!"

Trinity shook her head, and executed a perfect dive into the pool. She was surprised as she broke the surface; her hair had come loose in the water and now hung partially over her face. She hadn't realized that her RSI had changed, but she figured it made sense with everything that had happened in the past year.

"So," she said, making her way into shallower water and gesturing for Kid to follow, "how about you show me some of that aquatic combat now?"

"Ummm…uh…right. Well, you nod instead of bowing. Because if you were to bow in the water, you'd get water up your nose." Kid laughed nervously.

"Soooo _smart_," purred the woman in red.

Trinity shot her a death stare, and she closed her painted lips.

"All right, go ahead, Kid." She nodded deeply, feeling slightly ridiculous.

He charged forward yet again, looking ridiculous doing breast stroke, his legs flailing around in a clumsy frog kick. He obviously had not yet uploaded swimming skills. She let him get within striking distance of her this time before pushing off the bottom of the pool with all her might.

_Up_, she commanded her body wordlessly, and instantly the familiar rush was there. The air seemed to be rushing downward, an inverse current forcing her body up into the arc of the eagle. For a moment everything was deathly still and crystal clear, time holding its breath. She could see the drops of water hanging frozen beneath her.

Then just as suddenly, darkness, the grinding, hair-raising sensation of the data spike being removed, and she was back on the ship with Ghost standing over her.

"Captain? We've arrived."

She was on her feet in an instant, leaving the sounds of a groaning Kid behind her as she sprinted up the ladder to the cockpit. Neo was standing behind the copilot's chair, face ghastly white.

On the viewscreen, the machine city rose ominously before them, little bolts of purple energy flaring from time to time. There was an entire line of sentinels waiting around the perimeter to greet them.

* * *

Review please!


	9. A New Path

Author's Note: So now that my show is OVER OVER OVER I should have time to update regularly again. At least until AP exams start. Ugh. Oh well...four days until spring break. :D

* * *

Chapter 8

The sentinels began to move forward toward them, but at a much slower speed than usual. Neo leaned forward against the console, bracing himself. For a few fleeting seconds, he felt a stab of sadness that he could no longer see them in the golden corona of light that he had witnessed before. Now they were no more than little swirls of movement in the blur of color that made up his world. He could still feel them, though, he realized suddenly, though the connection had been weakened significantly. He closed his eyes and forced himself to focus, and immediately his senses were bombarded with a torrent of sights, sounds, emotions. It was the epitome of chaos, and it was utterly overwhelming.

"Neo?" Trinity's voice, through the storm, her hands on his back, steadying him. "You okay?"

He raised one palm for silence, struggling to gain control of the swirling vortex of perception. It was harder, somehow, than ever before, and he wondered if his abilities had been somehow permanently damaged, a remnant of the injuries he'd sustained in his duel with Smith. His head spun; his legs felt rubbery. He was dimly aware of Trinity helping him into the chair, but he did not dare break focus. He could feel one of the sentinels more powerfully than the others; it must

_We don't want to fight, _he thought, concentrating on getting the words or at least the intention across to the sentinel. _We just want to talk. Let us through._

One image grew out of the others, blossoming in the darkness against his closed eyelids. The gates lowering, and a pathway into the city, past all the sentinels, into the very heart of the city. The sight sent a shock through him; he'd been here before, at the very end.

And then just as suddenly, the image and the connection were gone and he fell back against the chair, opening his eyes and gasping for breath. His entire body felt utterly drained. Everyone was standing huddled in the entrance to the cockpit, staring at him. Kid's mouth was hanging open, and even Niobe looked moderately impressed.

"Neo?" Trinity stepped forward and brushed a hand across his forehead, much more than she ordinarily would have dared in public. "What did you see?"

"I don't know…" He shook his head and grasped loosely at her hand, letting her fingers slip through his. "But I think they'll let us in now."

"All right. Niobe, maintain our present course."

"Captain, are you sure?"

"Yes. Just take it slow."

There was a low rumbling noise from outside the ship, then a dull clunk, and the floor began to rock beneath their feet.

"What the—" muttered Link.

"They've latched onto our hull," answered Niobe.

"They're escorting us in," said Neo, for he was sure now that that was their intention.

He pushed himself up out of the chair with great effort, still weak from his ordeal. Trinity moved to help him, though discreetly, one hand on his arm, the other pressed against the small of his back. She led him back to their room, then deftly maneuvered him onto the bed, sitting down beside him and wrapping an arm around his waist.

"Are you sure you know what you're doing?" she whispered, leaning in to place a gentle kiss against his temple.

Neo laughed bitterly and turned into her touch, bringing one hand up to tangle in the hair at the nape of her neck.

"Hell no. But do I really have a choice? Like you said before, it's my duty. It's the only reason I'm here, as far as the Council and the people are concerned."

"Neo…I don't want you to feel like you have to do this. Not after last time."

He sighed, forcing himself to focus once more, fighting down nerves. He had no idea how he would find the strength to face the task before him, but he knew he could not live with himself if he backed down.

"Trinity…you know as well as I do that they won't talk to anyone else. I need to do this. For Morpheus. For you." He attempted a laugh to lighten the mood, but it failed miserably, breaking off into something like a sob. "Besides, I'll be fine as long as I don't close my eyes, right?"

"Neo…" She ran a hand up under his shirt, caressing the sensitive line of plugs there. "You're shaking."

He shivered under her touch, then leaned over and pulled her into a crushing embrace. He was painfully aware that he had been less than supportive lately, especially since the Athena had left Zion. He was torn every second she was in his sight now, wracked with guilt at the knowledge that he would be utterly unable to protect her if the need arose. He knew she would likely kick his ass if she ever found out, but still the feeling would not leave him alone.

"Neo…" Her voice was filled with concern; he knew she wanted him to talk, but he simply couldn't bring himself to face reality at the moment.

Neo leaned in and caught her lips wit his before she could manage another word. She stiffened against him at the initial contact, but he was used to this reaction by now. Though he had taken it as a bad sign at first, he'd come to realize that defense was her gut response to everything. It had become a sort of game he'd played with himself early on, racing to see how quickly he could get her to relax.

He mirrored her, slipping one hand up under her shirt and pressing his knuckles into the spot at the top of the line of plugs. She arched into his touch, moaning, and his pulse sped up. It had been far too long, he thought, since they'd been together like this. What privacy they'd had had been dedicated almost solely to comfort; survival. She was meticulously gentle with him always now, and on more than one occasion he'd caught her looking at him out of the corner of her eye, as though afraid he'd break or vanish into thin air. It was unnerving and heartrending to the extreme.

"Neo." She pulled away at last, holding his shoulders at arm's length. "We need to formulate some kind of a plan. We'll be there soon."

He took her by the wrists and gently removed her hands from his shoulders, clasping them in both of his and leaning back in to kiss her. He knew that she was right, but still couldn't bring himself to face the fear. Her fingers dug into his shoulders almost painfully, betraying her own misgivings. She pulled away again a moment later, but all attempts at steering the conversation back to the mission were gone, replaced by pure desire and need.

"Trin…" He stopped suddenly as the realization hit him. He knew that she expected him to go farther now, but he still was not ready. He hated the fact that he couldn't see, hated feeling so completely dependent. He knew that she would understand, but still couldn't bring himself to ask for help.

A sharp knock on the door broke the moment, bringing both disappointment and relief. He would have to face this another day. Until then…well, there were larger concerns to be dealt with. Trinity pulled away and went to answer the door.

"Yes, Link?"

Neo shifted uncomfortably on the bed, painfully aware that she had said Link's name only for his benefit.

"The machines are broadcasting, Captain. They say that if we are to have an audience with them, we must adhere strictly to their conditions."

"And those conditions are…?"

"They want to talk to Neo. Alone."

Trinity sighed loudly.

"That's not acceptable."

"They're not willing to negotiate."

"They'll have to."

"Captain…"

"I'm not going to let them manipulate me, Link."

"But Captain…"

"I'll go," said Neo loudly, forcing himself to stand. His knees felt rubbery, but he refused to let it show.

"Neo, you can't," said Trinity dismissively. "You can't even walk by yourself."

He knew she was only stating the facts, would never mean it in a hurtful way, but still the words stung like alcohol on an open wound.

"Let me go," he repeated. "You know we don't have a choice."

* * *

The air outside of the ship was deathly still, and felt charged with a strange foreboding. There was a slight metallic smell in the air, and it was oppressively hot. Thunderclouds roiled overhead in the dark sky. There was the anxious feeling of the calm before a storm, but there was no longer enough moisture left on the planet for rain.

Neo took a few tentative steps forward, hoping he was not about to fall off the edge of a cliff and plunge into the machine graveyard below. He hated the idea of facing the machines alone, unable even to see his enemy this time, but he knew it was a challenge he would have to face. Even Trinity could not deny the fact that they were helpless against the machines' terms. They needed information about the virus, and a violation of the delicate protocols they had established so far could have repercussions as far reaching as to jeopardize the delicate peace settlement.

Two cold metallic tentacles closed over his wrists, and Neo bit his lip to stifle a cry of surprise. The tentacles tugged a little, and he realized that he was expected to follow. The sentinel must have been sent to lead him to the place of rendezvous. It was the ultimate trust walk, he thought, blindly placing his life in the detached, logical control of his enemy. He took a few steps forward, slowly at first, then faster.

A few moments later the sentinel came to a halt and let go of Neo's wrists. One tentacle came forward to gently press on the center of his chest.

_Stop. _The word made its way into the periphery of his mind, along with an image of himself standing at the edge of a cliff.

"Thanks," he muttered in the direction he guessed the sentinel to be.

A dull roar filled his ears, then the deep, booming voice of Deus ex Machina.

"You return, human."

Neo forced himself to nod slowly, resisting the urge to turn and run. Before it hadn't mattered. Before there was nothing left to lose. Now he had every reason in the world to want to stay alive and in one piece.

"Your motive?"

"The people of Zion are falling ill," said Neo, careful to keep his voice neutral. The last thing he wanted was for the machines to take this inquiry as an unprecedented attack. "Some of the freeborns have been…infected with your pod technology. And those who were born in the powerplants are experiencing hallucinations of sorts. It's as if something is hacking their minds from inside the Matrix."

"Strange," said the voice noncommittally.

"Do you know what is happening?" asked Neo, feeling his stomach turn over dangerously. He knew he was on shaky ground pushing further, but they needed a definitive answer.

He was met with the words he had both hoped for and feared; the words that turned the end of one path into the beginning of another.

"We know nothing."

* * *

Review please!


	10. Higher Authority

Chapter 9: Higher Authority

"You can't be serious," protested Trinity as Neo finished relating his encounter with the machines to her. She was slightly upset with him for insisting that he go alone, though she was more irked at having to admit that he was right than at the outright act of going. Still, he had put himself in enough danger to considerably jangle her nerves, and, it now appeared, for relatively no useful information. "You really think they don't know?"

"Why would they lie to us?" Neo seemed surprised that anyone would even question the validity of the machines' claim.

Trinity sighed and took another sip of the lukewarm coffee in her mug. The entire crew was seated in the mess hall discussing their next plan of action. She hadn't really expected an easy answer, but the lack of any answer at all made her decidedly nervous. Her instincts told her the machines likely weren't innocent, but she knew that Neo was better attuned to them than she was. Her mind had been biased by years of war. Besides, to question the machines' honesty on one matter would bring it into question on every matter including the peace agreement. And that was the last thing anyone wanted.

"Oh, I don't know," said Sparks dryly. "Any reason from they get a kick out of it to they want to keep their city alive by sucking the living daylights from thousands of innocent humans. No offense, Neo, but why _wouldn't _they lie?"

"Hey," interjected Kid. "Leave him alone."

"Oh, so now you're the One's personal watchdog?" shot back Sparks.

"Leave _me _alone," said Kid, his voice rising in pitch and volume.

"Enough," said Trinity, running a hand irritably through her hair. "The last thing we need is to start fighting with each other."

"Thought this was a discussion," mumbled Sparks in a voice she could barely make out.

"Sparks," said Niobe, her eyes flashing dangerously.

"Sorry, captain," he muttered. It was unclear whether he intended this to Trinity or Niobe. Trinity decided to just settle for silence and not push it at the moment. There would be time for discipline later, if needed.

"All right then," said Niobe, taking control of the discussion momentarily. Trinity leaned back in her chair, mentally thanking her first officer. "We've got a problem here. The machines say they don't know anything. Some of us believe them. Some of us don't. What are we going to do about it?"

"Have one giant sparring match and see which side kicks the other's ass," muttered Sparks sarcastically.

"That's _enough_," warned Trinity, barely able to control the anger in her own voice. "Ghost? Link?"

Link shook his head, dark dreadlocks rearranging themselves on his shoulders.

"I don't like this. I don't like it one bit."

"Just what we need, another doomsday prophet," said Sparks. He melodramatically clamped a hand over his mouth as all eyes turned to glare at him.

"Ghost?" asked Trinity again.

Ghost shook his head thoughtfully.

"I don't know, Trinity. I can only suggest that you do what I do when I am in a difficult position."

"What's that?" she asked, curious despite herself. Ghost never failed to have an interesting answer.

"Seek the knowledge of a higher authority."

"Well, well," said Niobe, "that's the first valuable suggestion yet."

"So what then?" asked Kid nervously. "We go back to the Council?"

Trinity nodded slowly.

"I think that might be our best plan of action."

"Wait," said Neo, pushing back his chair. "We can't go to the Council yet. Not when we're fragmented like this. They'll tear us to bits in a matter of minutes."

"I don't think we really have a choice, now that you mention it. We're not authorized to act diplomatically besides getting what information we can, and probing farther will require discretion. You know Lock would throw us in the stockade without so much as a thought if he felt we were doing anything to jeopardize the peace."

Neo sighed, and she knew that she had won.

"Besides, we'll have plenty of time on the way back to agree on a concrete position," said Trinity, looking pointedly at Sparks. "Niobe, set in a course for Zion."

* * *

Niobe made her way into the Core silently, not wanting anyone aware of her presence immediately. She knew she should be making her way back to her cabin—it was already late at night—but somehow the day's events had sufficiently unsettled her to make sleep a faraway thought. Ghost was seated at the Matrix feed console, assigned the graveyard shift. He turned instinctively despite Niobe's attempted stealth.

"Captain?"

"Not anymore, Ghost," said Niobe quietly.

"Sorry…Niobe," said Ghost uncomfortably. "Old habits die hard."

Niobe sighed and sat down in the chair next to Ghost's. She had been debating whether or not to share her concerns with anyone, but Ghost had always been her most trusted officer, and she needed an unbiased opinion.

"What's wrong?" asked Ghost, reading her mind as always.

"Tell me, Ghost. What happened today? In that discussion?"

He sighed thoughtfully, dark eyes full of distance.

"Neo stood up for the hard side of the argument. Kid did what he does best, which is to follow blindly. Sparks panicked, and took it out on everyone in typical Sparks fashion. And Trinity…is trying very hard to run this ship diplomatically, though I think she'd much rather just act on her own instincts."

"And if she did? Would the crew support her?"

Ghost frowned at her.

"By Zion law, they would be required to."

Niobe smiled a little at his logic. Ghost was playing with her, in his own way, attempting to get more information out of her than she could get from him, though he'd never admit it.

"But would they?"

"What are you asking me, Niobe?"

"Are you and Sparks loyal to Trinity now, or to me?" said Niobe at last, through gritted teeth. "I'm not accusing you, Ghost, but as you said, old habits die hard."

"I am loyal to my captain," said Ghost noncommittally. "Sparks I cannot speak for." He reached forward and tapped a few keys, switching the search area on the monitors. It was an excuse to pause for a moment before he asked the next question. "What about you, Niobe? Who are you loyal to?"

Niobe resisted the urge to bite her nails, a childhood nuisance that resurfaced every once in a while when she was feeling the pressure especially severely. She hadn't wanted to admit it to herself, but it was exactly his question that had been haunting her since that afternoon.

"I'm loyal…to the truth," she said finally. "Whatever that means."

"But whose truth?" asked Ghost. "Would you go against your captain if it meant standing up for your truth?"

"Maybe," answered Niobe slowly. "I don't know, Ghost. She's a good captain, and a better friend, but this is just such a sticky situation. There are a million ways she could go wrong. Any one of us could. I don't know what I'd do if that's what it came down to."

"When the going gets tough…" said Ghost, offering her a hint of a smile.

Niobe laughed.

"Why, Ghost, I like your philosophy."

The smile blossomed into a rare grin.

"That has to be a first."

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Review please!


	11. Risk Assessmentpart 1

Author's Note: All right, so I apologize for the fact that this is only half a chapter. I'm going out of town and won't have a chance to update again until early next week, so I figured I'd post what I have so you wouldn't all think I'd died. I'll post the end as soon as I get a chance.

Also, I just posted a one-shot for Constantine, so check that out if you're interested.

Michelle

* * *

Chapter 10-1 –Risk Assessment

The beeping of the machines sounded like the ticking counter of a time bomb. Green lights flickered and pulsated on the displays like a million watchful, prying eyes. There was a mesh of wires leading to the bed. Trinity sighed and forced herself not to look away. The wires and machines gave Morpheus the appearance of a fly trapped in a spiderweb, helpless and unable to get free.

"Talk to me," said Neo coming to her side on the way back from his own appointment with the Zion medical staff. He'd insisted on coming into the quarantine ward with her even though he couldn't see. "Anything new?"

Trinity shook her head, then realized he couldn't see. She grabbed his hand and brought it to her lips, feeling unusually emotional. Morpheus had always been like a father to her; seeing her captain so utterly helpless was faith-shattering.

"No," she said softly. "Nothing. They're still watching. Trying to make sure that no one's going to hack into his mind and get the Zion access codes. I think they would try to change them, but that would require jacking in, and, well, that would go against the peace. You know that."

Neo sighed and slipped an arm around her waist. It occurred to her suddenly that she should ask him about his own news, but somehow she only felt exhausted.

_Get a grip, _she ordered herself. _You're in charge now. Get a grip or the price will be much, much higher._

"What did the doctors tell you?" she asked softly at last. "About your eyes?"

He sighed again, and Trinity knew that the news had not been what he was hoping for.

"They tried one more laser operation…helped a little…not enough."

She turned abruptly toward him, staring into the depths of unseeing hazel eyes.

"What are your options now?"

His hand found hers, wrapped around her fingers, tracing the shape of her palm. It was a long time before he answered, it seemed an eternity—almost long enough for her to lose her composure.

"There's one more operation they can try. Real surgery. But it's risky."

"How risky?"

"There…could be brain damage. I could lose my sight completely…worse…"

"Neo…" Trinity turned toward him, her fingers playing over his shoulders. She was struck by a wave of shyness momentarily—it suddenly seemed disrespectful to be having such a personal conversation in front of her albeit unconscious captain—but she shook it off quickly and forced herself to focus on Neo. "You don't have to do it, you know. I mean, I'll always be here for you."

He pulled away abruptly, as if sensing her discomfort.

"Trinity…I know that. And…without this sounding horrible, my decision isn't about you. It's about what I can and can't live with. Going on like this…I just don't think I could do it."

"So you're going to go ahead with the operation, then. For you." It came out more harshly than she'd intended, and she instantly regretted it.

"Yes," he muttered. "I have to."

"Neo…at least wait until…all this is over."

He nodded slowly, but didn't say anything—it was not exactly an agreement. She was about to say something else when they were interrupted by the sound of the door being flung open. She turned just in time to see one of Lock's assisstants entering.

"Captain? The Commander needs to see you in his office at once. He has…issues he would like to discuss with you."

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	12. Risk Assessment part 2

Author's Note: Here's the second half of the chapter. I'll probably consolidate them into one chapter on the site when I post Chapter 11. Sorry for the long wait. I know it's always an excuse, but I have AP board exams coming up in the next few weeks, so I'll be lucky if I get one fic updated each week. I'm sorry, but college credit just has to take precedence here. Come summer though, I should be able to update all I want.

:chants:

32days32day32days….

:falls over dead:

Michelle

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Chapter 10-2 –Risk Assessment

The door made a terrible grating noise as it swung open, like the hinges hadn't been oiled in a very long time and were slowly wearing down, weakening bit by bit, friction leading to the inevitable breakdown. Like the people of Zion, Neo thought as he guided himself into Lock's office, keeping one hand along the wall. This was the last place he wanted to be at the moment. He could practically feel the commander's eyes boring into him, sizing him up, deciding he was no longer fit for anything better than sitting around and aging in the bars like so many of the former Resistance soldiers.

"Neo, Trinity," came Lock's voice, cool and controlled to the extreme as always. "Thank you for coming, I'm sure you understand there are matters of critical interest at stake here."

"I'm not sure I do," said Trinity in an equally cold tone. "Could you please explain it to us, Commander?"

There was a moment of taut silence, then Neo heard Lock sigh.

"Sit down," ordered the Commander.

"I think I'd rather stand," said Trinity in an ultra-polite voice, and Neo had to smile. She was getting punchy, he thought, and he liked it.

"As you know, there will be a Council meeting tomorrow morning to finalize…plans for your ship, and a way to combat this…crisis. However, since there are more _personal _matters at stake for the two of you, I thought it might be appropriate to bring it to your attention now."

"Why don't you tell us why we're here, Commander?" said Neo. He had a feeling he wasn't going to like it.

There was the sound of things being shifted around on the desk, an excuse to prolong the silence. Neo found the back of one of the chairs with his left hand, ran his fingers over it. The back was cold, rough metal, the front cushioned by a thin padding and some rough-woven fabric. He made an attempt to picture the chair in his mind, was sure he had seen it before, but somehow couldn't quite manage to recall the color of it. It was a disconcerting realization, especially considering the news he'd just gotten from the doctors.

"As you understand, the Zion medical staff has been carefully monitoring the mind of your former Captain Morpheus. So far they do not believe that they have found any attempt from inside the Matrix to retrieve the Zion access codes. However, due to the strange nature of this…virus…I do not believe that we would necessarily be able to see such an attack."

"What are you saying?" asked Neo.

"I believe that we must take the safest possible course of action in order to protect our city. I believe we must eliminate the threat all together."

"Meaning…?"

"I believe it is necessary to have Morpheus' memory of the access codes destroyed."

"You can't do that," said Neo, gripping the back of the chair painfully. "That would kill him."

"If it means keeping the inhabitants of this city safe, then yes. That is what I believe is necessary."

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Review please! 


	13. The Assignment

Author's Note: Hey guys. Sorry this is so late. And that it's kind of boring. My brain is really fried. But this chapter needed to happen, and I promise it'll get more exciting soon.

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Chapter 11-The Assignment

The Council chamber was noticeably less populated than usual. The faces of the councilors who were present were grim, and there was little question as to the whereabouts of the absent members—more victims of the "virus."

Niobe took a seat in the front row between Sparks and Ghost. The rest of the crew was seated along the hard, cold bench to either side. The Council table rose above them, towering like a wall. Since the fleet no longer officially existed, there were no other captains to attend the meeting and fill the wall of metal bleachers reserved for them. The chamber seemed huge and cold. Full of ghosts. Breath seemed to echo off every hard surface.

"All rise," announced Councilor Hamann, "and let the meeting commence."

Niobe stood for a moment with the others but let her gaze remain on the floor. She had no wish to look at Lock who was seated at the end of the table.

"You may be seated," continued Hamann, and there was a distant shuffling noise as everyone complied. Hamann looked uncharacteristically nervous, thought Niobe. He was usually the epitome of calm; he practically radiated confidence. But today his face reflected only weariness and a quiet sense of unrest.

"The Council is gathered today to hear the official report of the crew of the Athena on their findings regarding the current health crisis afflicting this city during their trip to speak with the machines in their native area on the surface."

Niobe resisted the urge to roll her eyes. As much as the Council claimed to be progressive, the meeting tended to be painfully longwinded and old fashioned. Zion was a city built on tradition and the people were not about to let those traditions go no matter how ridiculously dated they had come to be.

"Yes, sir," said Neo, getting to his feet.

Niobe turned slightly toward him on the bench, noting Lock's glare with a touch of satisfaction.

"With all due respect, sir, I don't think that the answer I'm about to give you is the one the Council wants to hear. The machines no nothing of the illness here. They cannot be responsible if they have no knowledge of the situation."

"Now wait just a minute—" started Lock, getting to his feet.

Hamann held up a hand for silence. Lock shut his mouth abruptly, though he continued to glare. One of the other Councilors said something in a low voice, and Hamann leaned over to listen.

"This claim that the machines have made, their statement that they have no knowledge of the recent occurrences here," he said after a moment, "do you believe it to be true?"

"Sir, if I may?" Trinity broke in, standing up.

Hamann nodded, though Lock's face seemed to contract even further.

"While I will admit that I did not speak to the machines myself and have had no diplomatic contact with them personally, I find it quite difficult to believe that they are entirely innocent. My crew is split on the matter, however."

Neo flinched visibly, and Niobe resisted the urge to shake her head.

_What are you doing? _she thought, wishing telepathy was possible at the moment. _We agreed we were going to present a united front on the issue regardless._

"So you do or you do not believe the machines to be innocent?" repeated Hamann.

"I believe the machines to be innocent," said Neo simply, and sat back down.

"And you do not?" Hamann turned to Trinity.

"I…find it hard to believe that they have absolutely no knowledge of or involvement in the situation, yes."

Lock smiled at this; obviously he approved. The idea of the machines having no involvement must seem preposterous to him, thought Niobe. Anything at all unorthodox had always frightened Jason Lock to the extreme. Sentinels and agents he could deal with; the idea that the prophecy could be true—_that _was truly terrifying.

Councilor Hamann nodded once. "Thank you. You may be seated."

There was a long, uneasy silence as the Council members deliberated at their high table. Sparks tapped Niobe on the shoulder and leaned over to whisper to her.

"What's going on? This isn't the way it was supposed to happen."

Niobe shrugged.

"I don't know. I'm sure she has a plan. She knows what she's doing."

Sparks snorted and looked as if he wanted to say something else, but Niobe shushed him with an icy glare. A moment later, Hamann turned back to address the crew.

"The Council has reached an agreement. As I'm sure you all know, any attempt to jack into the Matrix and look further into this problem by either us or the machines would be in strict violation of the peace agreement. We are in a potentially grave situation here diplomatically. However, since this has the potential to be—already has been—extremely destructive to our city, the Council feels the need for further inquiry into possible involvement by the machines."

"Sir, what are you saying?" asked Trinity, a touch of impatience behind her normally cool voice.

"The Council has another assignment for you and your crew, if you would take it."

"What is it?"

"The Council requests that the Athena remain at broadcast depth for several weeks. Do not attempt to enter the Matrix. Simply monitor. Look for anything strange and any attempt to access it from outside by the machines. Report back."

"You want us to spy," said Trinity simply.

"Yes, in short."

"Do you really think that's wise?" asked Lock, getting to his feet again.

"That, Commander Lock, is not your decision," said Hamann. "Captain, do you and your crew accept this assignment?"

Trinity looked at Niobe and waited for her nod before answering.

"We do."

"Back to the sewers," muttered Sparks to Niobe. "Hallelujah."

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Review please! 


	14. A Choice

Author's Note: Sorry for the long wait. Hopefully I can get better about that now that it's summer. No promises though.

If you're enjoying this, go check out my stuff for Constantine. You know you want to. Go be good Matrix fans and support Keanu. And me. But mostly Keanu. Right.

Michelle

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Chapter 12: A Choice

"Back aboard the floating tin can again," muttered Sparks, flipping a card and grimacing. He'd been attempting to play solitaire for the past two hours, but hadn't yet managed to win a hand. "The odds are against me today."

"Statistically, the odds are always against you," said Ghost, looking up from his book.

"Why does that sound like a personal insult coming from you?" asked Sparks, flipping again, then giving up and shuffling the cards back into a pile in the center of the table.

Niobe glanced at them out of the corner of her eye, but resisted the urge to speak. She'd come down here for some peace and quiet in which to study some technical maps of the sewers—really just to get out of the confines of her room—but she was finding it impossible to concentrate. Still, the sound of voices, even theirs, beat the groaning of the engines.

"Take it as you will," said Ghost, his attention back on his reading.

Sparks shuffled the cards an extra time, letting the little bit of wind from them hit his face. They'd been in the tunnels for three weeks now without seeing any action, or any real activity at all for that matter, and the stuffiness was beginning to get to everyone. It seemed less and less likely that whatever was afflicting the Zionites was being caused by anything down here—there didn't appear to be anything more sentient than some bacteria which fed on rust. But still the calls came from the core, more and more taken ill by the disease. People were more than beginning to panic. It was surreal for the crew of the Athena, being trapped amidst dark, silent, floating waste and scrap piles from the war, hoping for some kind of action to keep them from going stir crazy. Hard to believe that only a few hundred miles away, thousands were dying.

Sparks spread his cards on the table, flipped one over, picked one up. Groaned again.

"Go fish," he said to himself, and Ghost looked up again, shaking his head.

"You know talking to yourself is never a good sign," said Niobe. They both turned and looked at her. She shrugged.

"Only person down here who hasn't told me to shut up yet," countered Sparks.

Niobe rolled her eyes.

"Getting acquainted with one's inner self can be a rewarding experience," said Ghost. "However talking may not be the best way of going about the task." With that he shut his book, got up, and left the mess hall.

Sparks blinked.

"Was he just mocking me?"

Niobe shook her head.

"We may never know."

"So what's the plan, Cap—"

"Sparks…"

"Niobe. Sorry. What's the plan? How long are we going to be rotting down here before we can conclude that nothing's going on?"

She sighed.

"You know as much as I do, Sparks. Until the council comes up with a better plan of action."

Kid walked in then, holding the Rubik's cube, his entire attention focused on it. It was still as scrambled as it had been before, if not more so.

"Luck?" asked Sparks, smirking.

"No," snorted Kid. "I think I'm just making it worse."

"You seem to be good at that," said Sparks. "I mean, in general."

"Hey!"

"Boys…"

"Aw, come on, Niobe. You said it yourself. You're not the captain anymore."

"I'm still your senior officer. And the last thing we need is to start needling one another."

They'd been passing the Rubik's cube around the ship for the past several weeks, but no one had had any amount of success with it. It seemed as though the fates were teasing them, using the cube as a metaphor for their entire fruitless mission.

"Niobe?" said Link, sticking his head in the door. His usual warm voice sounded oddly strained.

"Yes?" She folded the maps and looked up, his tone making her heart speed up. Much as she'd hoped for action of some kind to alleviate the boredom, a crisis right now was anything but an inviting prospect.

"I think you'd better come to the Core. We've got…a bit of a…just come."

Niobe got to her feet and followed Link through the twisting hallways of the ship, leaving her maps folded on the table. There were only two possibilities here: either they'd gotten word from the Council, or they'd come upon something that could possibly explain the crisis in Zion.

Neo and Trinity were seated around one of the monitors as Link and Niobe entered, locked intently in what appeared to be a discussion hinging on argument. Neither one looked at all happy.

"The Council must have approved it. He couldn't have just acted without them," said Neo quietly.

"Doesn't matter," answered Trinity. "The Council is in Lock's pocket. Has been for months now. Everyone has forgotten how terribly he performed in the war already. That's the entire reason we're out here wasting time instead of back there where we could actually be doing some good."

"Then we have to stop wasting time," said Neo.

Link started to speak, but Niobe held up a hand for him to be quiet. The others hadn't noticed their presence yet, and suddenly she wasn't eager to interrupt.

"What are you saying?" asked Trinity sharply.

"That we get to the bottom of this."

"By jacking in."

"If that's what it takes."

"You know we can't do that. It would be a violation of the Peace."

"So is what we're doing now. People are dying. We have to risk it."

"You wanted to see me, captain?" said Niobe, breaking in at last.

Trinity jumped, looked up sharply, then shook herself and nodded.

"Yes. We've received some disturbing news from the Council, and we need to decide what plan of action—"

"What kind of news?" asked Niobe, suddenly very afraid of the answer.

"Things have gotten so bad that…Commander Lock…felt it was necessary to carry out his plan of defense—"

"Morpheus is dead," said Neo bluntly.

Niobe felt as though she had just been punched in the stomach. The walls had just collapsed on their mission—there would be no more waiting around. There would be a simple choice now—obey a commander who had just for all intents and purposes committed cold blooded murder, or take their chances in violation of the law.

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Review please! 


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